The HudsonAlpha Genome Sequencing Center advances genomic sciences for plants and fungal species that are important for food production and renewable biofuel research. The goal of the GSC is to rapidly accelerate the understanding of biological systems using genomic approaches, including tools such as reference genomes, transcriptomics and comparative sequencing; and collaborating with groups to apply this knowledge to solve current, real-world problems. 
In recent years the GSC has concentrated on producing high quality, reference plant genomes as part of the U.S. Department of Energy Joint Genome Institute. In the cases of crop species such as sorghum, soybean, peach, citrus and millet, these genomic references form the basis for genomics-enabled crop breeding to increase yields and reduce pesticide and water use. 
Current projects, with collaborators spanning plant breeders to genomic scientists, apply genomic methods to accelerate the domestication of energy crops such as switchgrass, poplar and eucalyptus. The lab has also been developing models for bioenergy grass work with Brachypodium, panicgrass and green foxtail that will enable rapid advances in understanding the biology of cell wall formation which is fundamental to extracting sugars from plants that can be converted to liquid fuel. 
Major funding for the GSC comes from the U.S. Department of Energy’s Biological and Environmental Research Program which supports scientists working in the areas of sustainable biofuel production, improved carbon storage or contaminant bioremediation.
Lab members represent a blend of experienced molecular biologists, data analysts and computational scientists who work on cutting edge genomic techniques. According to HudsonAlpha faculty investigators Jeremy Schmutz and Jane Grimwood, Ph.D., the GSC is one of the leading labs in the world in the assessment, sequencing, assembly and improvement of large eukaryotic fungal and plant genomes. Scientific products directly affect plant biologists, crop breeders, farmers and agricultural companies and will eventually change the way society interacts with the environment.
Cacao genome sequence could have sweet results for growers
HudsonAlpha, in partnership with MARS, Inc., the USDA, IBM and Clemson, Indiana and Washington State universities, is learning more about the cacao genome and sharing that knowledge to improve the way breeders and farmers harvest the crop. 
The GSC assembled the cacao genome, as well as the chromosome scale reconstructions to produce the final reference sequence. 
Through cacao genome sequencing, researchers learned why some cacao variations are optimal for breeding, yet produce an undesirable flavor or aroma. Other variations, when combined with different beans, increase flavor and color yet decrease the quality. Additionally, sequencing has identified resistance to various diseases and other horticultural traits. 
“Cacao is a major export of many African and Asian countries and is a high value crop. The genomics work, combined with breeding programs, forms the basis for maintaining and improving the stability of the cacao supply,” said Jeremy Schmutz, faculty investigator. 
The preliminary results from the sequencing were published in 2010 with the full results being released in 2013. Farmers on the Indonesian island of Sulawesi are already benefitting from the research by learning new processes for sustainable farming. 
The publication, The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color, is found in Genome Biology, released 3 June.
Stress biology research to improve crop plants
Some plants – called halophytes – can grow in soil with high concentrations of salt. The HudsonAlpha GSC worked with associates at the University of Arizona, Duke University and the DOE Joint Genome Institute to assemble a reference genome for the halophyte Eutrema salsugineum toward determining mechanisms for crop plants to grow under a wide variety of conditions that typically limit crop productivity. 
E. salsugineum is a species in the Brassicaceae that naturally tolerates multiple environmental stresses. Researchers compared E. salsugineum with its close relative Arabidopsis thaliana, looking at genome structures, protein-coding genes, microRNAs, stress-related pathways and estimated translation effi ciency of proteins. 
The research suggested that adaptation to environmental stresses such as salinity and cold may occur through a global network adjustment of multiple regulatory mechanisms – both evolutionary and molecular. The E. salsugineum genome provides a resource to identify naturally occurring genetic alterations contributing to the adaptation of halophytic plants to salinity; these alterations could potentially be introduced in related crop species. The reference genome of the halophytic plant Eutrema salsugineum was published this spring in Frontiers in Plant Science.
Selfers and crossers — a study of Shepherd’s Purse
About 200,000 years ago, Capsella rubella, commonly known as Red Shepherd’s Purse began self fertilizing and split from C. grandiflora. To study the effects of selfing on C. rubella’s genome, HudsonAlpha, DOE JGI and other partners in the U.S. Canada, Europe, China and the Middle East sequenced and compared it with C. grandiflora and members of the closely related Arabidopsis genus – the first plant ever sequenced and a model species for plant genomics. The study was published 9 June in Nature Genetics.
C. rubella showed a mass decline of the removal of harmful mutations without a naturally occurring alteration in the amount of genes present that can move between chromosomes. From these findings, it is theorized that a dramatic event left C. rubella in a situation where a need for pollinators outweighed the known negatives of inbreeding and caused the C. rubella to shift into selfing. Though this caused the C. rubella to face a bottleneck, its ancestral genome structure remained intact. 
“The factors driving such contrasting modes of genome expansion and shrinkage are far from resolved, and it will be important to broaden future comparisons to better understand the processes driving genome structure evolution,” the team said on the study’s conclusion and future plans.
They added that with many crops known to be self-fertilizing, the study highlights the importance of preserving crop genetic variation to avoid losses in yield due to mutations accumulating. Notably, ancient self-fertilizing lineages are rare and support the reasoning that the process is an evolutionary dead-end.
Training the next generation
Chalmers, 20, is a biomedical engineering major at Mississippi State but is from Madison, Ala. He heard about HudsonAlpha’s BioTrain internship program while attending Bob Jones High School and knew it was a challenge he wanted to accept. “I was really looking for someplace to grow, a field I wasn’t too comfortable with yet,” Chalmers said. “I wanted to know if this was something I wanted to pursue. It’s been enjoyable because it’s been a real challenge.”
Robbie Chalmers supported researchers’ efforts in the GSC. His enthusiasm for learning is tangible when he discusses his lab assignments. “We worked on plants and plants have an interesting complexity to them,” he said. “Their genomes aren’t the simplest to sequence, so I worked on building a tool to make what the researchers are doing easier by helping simplify the genome.” 
According to Chalmers, the benefits of BioTrain included working in many new situations and being exposed to different people, projects and labs. After college, he plans to attend graduate school and then see the world. “Research opportunities in Antarctica have come up recently, and I thought that would be interesting.”